1. Tests of diversity / tree shape
2. Tests of rates
Test: is there less genetic diversity than expected?
Influenza phylogeny and effective number of infections
Coalescent rates in flu and measles
Selective sweeps purge nearby diversity
Depth and breadth indicates age and strength of sweep
Selective sweeps purge diversity in Drosophila
Test: is the tree shape different from the neutral expectation?
Tajima's D statistic summarizes deviation from neutrality
Influenza has negative Tajima's D
Test: is there an overabundance of fixed non-synonymous mutations?
"Trunk" branches show an excess of non-synonymous change at epitope sites in influenza